Free University Amsterdam, Amsterdam, The Netherlands

vuamsterdamDescription of organisation

The department of Molecular Cell Biology and in particular its sections on Microbial Physiology and Systems Bioinformatics constitute one of the European strongholds in Systems Biology, with Frank Bruggeman, Bas Teusink, Jacky Snoep, and Hans Westerhoff as its best known PIs in that field. This group has also been seminal to and is part of the Netherlands Institute for Systems Biology (NISB). The overall research goal is to show how a scientific focus on interactions in complex biological systems leads to the discoveries of new principles behind the emergence of important biological functions such as health. Failure of those principles, due to mutations or abnormal environmental effects, are then shown to cause disease. In addition it is shown how network rather than single molecule targeting may lead to more effective therapies and reduced toxicity. Frank Bruggeman is a highly effective group leader in the NISB, a close association of the VUA, the University of Amsterdam, and the Centre for Mathematics and Informatics (CWI). Bruggeman is a leader in the modelling of the integration between gene expression, signal transduction and metabolism, both in terms of average behaviour and in terms of noise. Snoep is the driver behind the live model repository JWS-Online. Through Bruggeman and Teusink the group is involved in much Dutch Systems Biology. Through Dr Jeantine Lunshof the department is associated with the groups of George Church in Boston and of Angela Brand in Maastricht. Through Hans Westerhoff there is a personal union with the Manchester Centre for Integrative Systems Biology at UNIMAN (participant 5).


Previous experience

Frank Bruggeman has been intensely involved in the EU Network of Excellence BioSimulation, in which

more than 30 scientific groups collaborated to promote the simulation of biological processes in the context of drug targeting and disease. Dr Bruggeman also led the Amsterdam leg of the Marie Curie Training Network for Nuclear Hormone Receptor Systems Biology, where he and his two Ph D students had the arduous task of modeling the experimental systems of more than 15 experimental partners. He is now (co-) leading more than 10 research projects with various experimental scientists in and around the Netherlands Institute for Systems Biology. His group has strong expertise in the modelling of both noise and average function in gene-expression systems, transcription dynamics, metabolic and signal transduction pathways, and cell-cell interactions. Bas Teusink is co-director of the Kluyver Centre for Microbial Genomics and Systems Biology, and acting director of the NISB.


Profile of staff members

Frank Bruggeman is group leader at the NISB and a young but internationally already well-known expert in Systems Biology. Bas Teusink is Professor of Systems Bioinformatics at the VUA and first author of one of the first systems biology papers with an experiment-based mathematical model of the dominant metabolic pathways of an organism. Since then he has also been developing many new ways of performing and interpreting flux balance analysis. He has interests in the Warburg effect of tumors. Hans Westerhoff has a 30 % appointment as Professor of Microbial Physiology at the VUA, as well as an appointment at partner 5 (UNIMAN). Also Jacky Snoep holds Chairs at these two Universities, as well as at the University of Stellenbosch, South Africa.



Free University Amsterdam



Five recent publications relevant to the project

1. Kolodkin A.N., Bruggeman FJ., Plant N, Moné MJ, Bakker BM, Campbell MJ, Van Leeuwen JPTM, Carlberg C, Snoep JL and Westerhoff HV (2010) Design principles of nuclear receptor signaling: how complex networking improves signal transduction. Mol. Systems Biology 6; doi 0.1038/msb.2010.102


2. Teusink B, Westerhoff HV & Bruggeman FJ (2010) Comparative systems biology: from bacteria to man. Wiley Interdisciplinary Reviews-Systems Biology and Medicine 2, 518-532.


3. Conradie R, Bruggeman FJ, Ciliberto A, Csikasz-Nagy A, Novak B, Westerhoff HV & Snoep JL (2010) Restriction point control of the mammalian cell cycle via the cyclin E/Cdk2:p27 complex. FEBS J 277, 357-367.


4. Dobrzynski M & Bruggeman FJ (2009) Elongation dynamics shape bursty transcription and translation. Proceedings of the National Academy of Sciences of the United States of America 106, 2583-2588.


5. Bruggeman FJ, Bluthgen N & Westerhoff HV (2009) Noise Management by Molecular Networks. Plos Computational Biology 5.